Genome-wide Association Study Of Grain Quality Traits In Maize Inbred Lines

High yield,stable production,quality is the main goal of today’s corn breeding,and the grain is the final embodiment of yield and quality.In order to achieve high quality breeding objectives,we must research the quality traits of corn kernels,and use molecular markers to locate the key genes regulating maize grain quality,and to clarify the genetic mechanism from the molecular level,which can improve the efficiency of maize quality breeding.In this experiment,80 maize core inbred lines of Jilin Province were used as the research materials.Field experiment was conducted at the experimental sites of Jilin Agricultural University in 2014 and 2015,and randomized block test was designed.Test field management was the same as field.Every year,the self-pollinated test material was dried and threshed,and its protein content,fat content and starch content were determined by NIRFlex N-500 Fourier transform near-infrared spectroscopy from Switzerland BUCHI.Whole genome resequencing of 80 maize core inbred lines was carried out by Next Generation Sequencing(NGS),1,490,007 high quality SNPs were obtained,and subsequent association analysiswas performed.The results show:1.From the phenotypic data,the range of variation is larger,showing a large phenotypic difference,it showed that the protein content,fat content and starch content of different inbred lines were different and the degree of dispersion was higher.Pearson correlation analysis showed,protein content and fat content reached a very significant level,starch phenotype data reached a significant level,indicating that the correlation of the three traits in the two years was high,it ensures the accuracy of subsequent experiments.At the same time two years of the F value has reached a very significant degree,the measured data is more accurate,which can contribute to the follow-up of genome-wide association analysis.By calculating the generalized heritability,phenotypic variation was influenced by genetic factors.Combining the phenotypic variation range and heritability,this research is more suitable for the study of the genetic mechanism of these three traits by genome-wide association analysis.2.The association analysis showed that 11 SNP sites were significantly associated with the protein content of the seeds(P<0.000001),Which is highest locating in chromosome frame 3.04 SNP,it explained 85.76% phenotypic contribution rate.Four candidate genes were identified in the linkage disequilibrium region(5.2kb)of the significant SNP locus.Encoding RING-H2 finger protein,NET superfamily protein,COP9 signal transducer and hypothesis protein without characteristic function were predicted by these genes,these candidate genes may be closely related to the metabolic synthesis of proteins.3.The results showed that 10 SNPs were significantly correlated with the fat content of grains(P<0.000001).The SNP phenotypecontribution rate of chromosome frame bin 4.01 was the highest at 34.5% and the two candidate genes were excavated at that site.The two loci located in the chromosome frame bin1.10 belong to the same QTL.The QTL is repeatedly detected within two years.Six candidate genes were identified in the linkage disequilibrium region(5.2 kb)of the significant correlation SNP locus(P <0.000001),and the MYB transcription factors,pectinase,glutamine synthetase and three no-characteristic function of the presumed proteins were predicted,it may be closely related to the metabolic synthesis of fat.The results of this study lay the foundation for molecular marker-assisted selection of high-oil maize material and cloning important genes for controlling the synthesis of maize grain fat.4.The results of association analysis showed that nine SNP loci were significantly associated with the starch content of the seeds(P <0.000001),and the SNPs located at chromosome frame 3.09 explained the highest phenotypic contribution rate of 38.31%.Three candidate genes were excavated in the linkage disequilibrium region(5.2 kb)of the significant SNP locus(P <0.000001),which can predicte to encode N-acetylglucosaminyltransferase,signal recognition particles and no characteristic function of the presumed proteins,these candidate genes may be closely related to the metabolic synthesis of corn starch.The results of this study provide a basis for molecular marker-assisted selection of good quality maize varieties and good genes related to cloning quality traits of maize.